Two chloroplast genomes with reduced inverted repeat regions in Mammillaria series Stylothelae (Cactaceae)

Abstract

Background: The chloroplast genomes of Cactaceae exhibit boundary modifications in the inverted repeat regions (IRs), gene inversions, and deletions. Among nine Mammillaria species, three distinct chloroplast structures have been identified, although not all of these correspond to the morphology-based classification of the genus.
 Question: Is there a distinct chloroplast genome structure in the species of Mammillaria series Stylothelae?
 Studied species: Mammillaria bocasana and M. erythrosperma.
 Study site and dates: Mexico from 2019 to 2023.
 Methods: Chloroplast DNA was sequenced, and chloroplast genomes were de novo assembled using the Fast-Plast program. Complete plastome sequences were annotated and verified. The sequences were aligned in MAUVE program to detect possible structural changes. A maximum likelihood phylogeny was executed to evaluate the relationships of the studied species.
 Results: The plastomes ranged from 107,368 bp in Mammillaria bocasana to 108,069 bp in M. erythrosperma. Both presented a quadripartite structure and contained 108 genes. The IRs were ~ 1,600 bp long and included the genes rpl2, rpl23 (pseudo), and trnI-CAU. MAUVE identified a ~ 21 kb inversion in the large single copy containing a block of genes related to photosynthesis. The phylogenetic analysis placed both species in a single clade separated from the other species within Mammillaria subg. Mammillaria.
 Conclusions: The studied species of Mammillaria series Stylothelae exhibited a different and synapomorphic chloroplast genome structure. Other Mammillaria chloroplast genome structures have evolved independently in different lineages.